We expect most roxygen2 users will write documentation using markdown rather than Rd syntax, since it’s familiar, and doesn’t require learning any new syntax. In most cases, you can just use your existing RMarkdown knowledge and it’ll work as you expect. When it doesn’t, you can read this vignette to figure out what’s going on and how to fix it.
To turn on Markdown support for a package, insert this entry into the
DESCRIPTION file of the package:
Roxygen: list(markdown = TRUE)If you use devtools/usethis, this will be automatically inserted for
you when you create a new package. If you’re updating an existing
package, we recommend usethis::use_roxygen_md() which will
modify the DESCRIPTION and prompt you to use the roxygen2md package to convert
your existing docs.
If needed, you can also use @md or @noMd to
turn markdown support on or off for a documentation block.
Here is an example roxygen chunk that uses Markdown.
#' Use roxygen to document a package
#'
#' This function is a wrapper for the [roxygen2::roxygenize()] function from
#' the roxygen2 package. See the documentation and vignettes of
#' that package to learn how to use roxygen.
#'
#' @param pkg package description, can be path or package name. See
#' [as.package()] for more information.
#' @param clean,reload Deprecated.
#' @inheritParams roxygen2::roxygenise
#' @seealso [roxygen2::roxygenize()], `browseVignettes("roxygen2")`
#' @exportroxygen uses the commonmark package, based on the “CommonMark Reference Implementation”. See https://commonmark.org/help/ for more about the parser and the markdown language it supports. The most important details are described below.
The usual Markdown heading markup creates sections and subsections.
Top level headings (e.g. # title) create sections with the
\section{} Rd tag. This largely supersedes use of the older
@section tag.
Top-level headings can only appear after the
@description and @details tags. Since
@details can appear multiple times in a block, you can
always precede a ‘#’ section with @details, if
you want put it near the end of the block, after @return
for example:
#' @details
#' Trim the leading and trailing whitespace from a character vector.
#'
#' @param x Character vector.
#' @return Character vector, with the whitespace trimmed.
#'
#' @details # This will be a new section
#' ...Top level sections are placed at a fixed position in the manual page,
after the parameters and the details, but before \note{},
\seealso{} and the \examples{}. Their order
will be the same as in the roxygen block.
Headings at level two and above may appear inside any roxygen tag
that formats lines of text, e.g. @description,
@details, @return, and create subsections with
the \subsection{} Rd tag.
#' @details
#' ## Subsection within details
#' ### Sub-subsection
#' ... text ...For emphasis, put the text between asterisks or underline characters. For strong text, use two asterisks at both sides.
#' @references
#' Robert E Tarjan and Mihalis Yannakakis. (1984). Simple
#' linear-time algorithms to test chordality of graphs, test acyclicity
#' of hypergraphs, and selectively reduce acyclic hypergraphs.
#' *SIAM Journal of Computation* **13**, 566-579.#' See `::is_falsy` for the definition of what is _falsy_
#' and what is _truthy_.Inline code is supported via backticks.
#' @param ns Optionally, a named vector giving prefix-url pairs, as
#' produced by `xml_ns`. If provided, all names will be explicitly
#' qualified with the ns prefix, i.e. if the element `bar` is defined ...For blocks of code, put your code between triple backticks:
#' ```
#' pkg <- make_packages(
#' foo1 = { f <- function() print("hello!") ; d <- 1:10 },
#' foo2 = { f <- function() print("hello again!") ; d <- 11:20 }
#' )
#' foo1::f()
#' foo2::f()
#' foo1::d
#' foo2::d
#' dispose_packages(pkg)
#' ```You can also include executable code chunks using the usual knitr syntax. See below for more details.
Regular Markdown lists are recognized and converted to
\enumerate{} or \itemize{} lists:
#' There are two ways to use this function:
#' 1. If its first argument is not named, then it returns a function
#' that can be used to color strings.
#' 1. If its first argument is named, then it also creates a
#' style with the given name. This style can be used in
#' `style`. One can still use the return value
#' of the function, to create a style function.#' The style (the `...` argument) can be anything of the
#' following:
#' * An R color name, see `colors()`.
#' * A 6- or 8-digit hexa color string, e.g. `#ff0000` means
#' red. Transparency (alpha channel) values are ignored.
#' * A one-column matrix with three rows for the red, green,
#' and blue channels, as returned by [grDevices::col2rgb()].Note that you do not have to leave an empty line before the list. This is different from some Markdown parsers.
Use GFM table formatting:
| foo | bar |
| --- | --- |
| baz | bim |By default, columns are left-aligned. Use colons to generate right and center aligned columns:
| left | center | right |
| :--- | :----: | ----: |
| 1 | 2 | 3 |Markdown hyperlinks work as usual:
#' See more about the Markdown markup at the
#' [Commonmark web site](http://commonmark.org/help)URLs inside angle brackets are also automatically converted to hyperlinks:
#' The main R web site is at <https://r-project.org>.Markdown syntax for inline images works. The image files must be in
the man/figures directory:
#' Here is an example plot:
#' Markdown notation can also be used to create links to other help topics. There are two basic forms:
[topic]: The link text is automatically generated from
the topic.[text][topic]: You supply the link text.First we explore the simplest form: [ref]. The presence
of trailing parentheses, e.g., [func()], signals that the
target func is a function, which causes two things to
happen:
func() is automatically typeset as
code.| Markdown | Links to help topic for … |
Notes |
|---|---|---|
[func()][pkg::func()] |
a function in same package or in pkg |
Always typeset as code. Produces Rd: \code{\link[=func]{func()}}or \code{\link[pkg:func]{pkg::func()}} |
[thing][pkg::thing] |
a topic in same package or in pkg |
Use for a dataset or general doc page. Not typeset as code. Produces Rd: \link{thing} or\link[pkg:thing]{pkg::thing} |
[`thing`][`pkg::thing`] |
a topic in same package or in pkg |
Same as above, but explicit backticks mean that it is typeset as code. Good for documenting a class. Produces Rd: \code{\link{thing}} or\code{\link[pkg:thing]{pkg::thing}} |
Use the second form [text][ref] to link to the topic
specified by ref, but with text as the link
text.
| Markdown | Links to help topic for … |
Notes |
|---|---|---|
[text][func()][text][pkg::func()] |
a function in same package or in pkg |
Text is not typeset as code. Produces Rd: \link[=func]{text} or\link[pkg:func]{text} |
[text][thing][text][pkg::thing] |
a topic in same package or in pkg |
Text is not typeset as code. Use for a topic that documents NULLand name is set via @name,e.g., a dataset or concept. Produces Rd: \link[=thing]{text} or\link[pkg:thing]{text} |
[`text`][thing][`text`][pkg::thing] |
a topic in same package or in pkg |
Same as above, but explicit backticks mean that text is typeset as code. Produces Rd: \code{\link{=thing}} or\code{\link[pkg:thing]{pkg::thing}} |
Links to operators or objects that contain special characters do not
currently work. So to link to (e.g.) the %>% operator in
the magrittr package, instead of
[magrittr::%>%], you will need to use the
Rd notation:
\code{\link[magrittr]{\%>\%}}.
You can insert executable code with ```{r}, just like in
knitr documents. For example:
#' @title Title
#' @details Details
#' ```{r lorem}
#' 1+1
#' ```
#' @md
foo <- function() NULLbecomes:
% Generated by roxygen2: do not edit by hand
% Please edit documentation in ./<text>
\name{foo}
\alias{foo}
\title{Title}
\usage{
foo()
}
\description{
Title
}
\details{
Details
\if{html}{\out{<div class="sourceCode r">}}\preformatted{1+1
#> [1] 2
}\if{html}{\out{</div>}}
} This code is run every time you call roxygenize() (or
devtools::document()) to generate the Rd files. This
potentially makes roxygenize() (much) slower. Either avoid
expensive computations, or turn on knitr caching with
cache = TRUE. Make sure to omit the cache from the package
with usethis::use_build_ignore().
Note that knitr will call the appropriate print() or (if
available) knitr::knit_print() method on the result. This
may geenrate markdown not supported by roxygen2. If needed, override the
automatic methods to have your R calls return your own markdown as a
character vector, wrapped in knitr::asis_output().
Code blocks support some knitr chunk options, e.g. to keep the output
of several expressions together, you can specify
results="hold":
#' ```{r results="hold"}
#' names(mtcars)
#' nrow(mtcars)
#' ```Some knitr chunk options are reset at the start of every code block,
so if you want to change these, you’ll have to specify them for every
chunk. These are currently error, fig.path,
fig.process, comment,
collapse.
Alternatively, you can set the knitr_chunk_options
option to override these defaults, or add new chunk options that are
used for the whole package. See ?load_options for
specifying roxygen2 options.
Plots will create .png files in the
man/figures directory with file names coming from the chunk
name. Be aware that plots can quickly increase the size of your package
leading to challenges for CRAN submission.
#' ```{r iris-pairs-plot}
#' pairs(iris[1:4], main = "Anderson's Iris Data -- 3 species",
#' pch = 21, bg = c("red", "green3", "blue")[unclass(iris$Species)])
#' ```By default roxygen2 only includes PDF images in the PDF manual, and
SVG images in the HTML manual. If you want to avoid this restriction,
set the restrict_image_formats roxygen2 option to
FALSE, see ?load_options.
Rd markupNote that turning on Markdown does not turn off the standard
Rd syntax. We suggest that you use the regular
Rd tags in a Markdown roxygen chunk only if necessary. The
two parsers do occasionally interact, and the Markdown parser can pick
up and reformat Rd syntax, causing an error, or corrupted manuals.
Leading white space is interpreted by the commonmark parser, but is
ignored by the Rd parser (except in
\preformatted{}). Make sure that you only include leading
white space intentionally, for example, in nested lists.
The commonmark parser does not require an empty line before lists, and this might lead to unintended lists if a line starts with a number followed by a dot, or with an asterisk followed by white space:
#' You can see more about this topic in the book cited below, on page
#' 42. Clearly, the numbered list that starts here is not intentional.